Transcriptome Analysis of Spermophilus lateralis and Spermophilus tridecemlineatus Liver Does Not Suggest the Presence of Spermophilus-Liver-Specific Reference Genes

The expressions of reference genes used in gene expression studies are assumed to be stable under most circumstances. However, studies had demonstrated that genes assumed to be stably expressed in a species are not necessarily stably expressed in other organisms. This study aims to evaluate the likelihood of genus-specific reference genes for liver using comparable microarray datasets from Spermophilus lateralis and Spermophilus tridecemlineatus. The coefficient of variance (CV) of each probe was calculated and there were 178 probes common between the lowest 10% CV of both datasets (). All 3 lists were analysed by NormFinder. Our results suggest that the most invariant probe for S. tridecemlineatus was 02n12, while that for S. lateralis was 24j21. However, our results showed that Probes 02n12 and 24j21 are ranked 8644 and 926 in terms of invariancy for S. lateralis and S. tridecemlineatus respectively. This suggests the lack of common liver-specific reference probes for both S. lateralis and S. tridecemlineatus. Given that S. lateralis and S. tridecemlineatus are closely related species and the datasets are comparable, our results do not support the presence of genus-specific reference genes.

Preference of IRES-mediated initiation of translation during hibernation in golden-mantled ground squirrels, Spermophilus lateralis

Mammalian hibernation involves virtual cessation of energetically consumptive processes normally vital to homeostasis, including gene transcription and protein synthesis. As animals enter torpor, the bulk of initiation of translation is blocked at a body temperature of 18°C in golden-mantled ground squirrels [ Spermophilus (Callospermophilus) lateralis ]. Previous data demonstrated regulation of cap-dependent initiation of translation during torpor. We asked what happens to cap-independent, specifically, internal ribosome entry site (IRES)-mediated initiation of translation during hibernation. We analyzed polysome fractions for mRNAs that are known to contain or not to contain IRES elements. Here, we show that mRNAs harboring IRES elements preferentially associate with ribosomes as a torpor bout progresses. Squirrels allowed to naturally complete a torpor cycle have a higher IRES preference index than those animals that are prematurely aroused from torpor. Data indicate that this change in preference is not associated with gene expression, i.e., change is due to change in mRNA association with ribosomes as opposed to mRNA abundance. Thus, although processes like transcription and translation are virtually arrested during torpor, ribosomes are preferentially loaded with IRES-containing transcripts when squirrels arouse from torpor and translation resumes. Differential translation of preexisting mRNAs may allow for the preferential production of key stress proteins critical for survival of physiological insults that are lethal to other mammals.

Response of small mammals to alternative stand structures in the mixed-conifer forest of northeastern CaliforniaThis article is one of a selection of papers from the Special Forum on Ecological Studies in Interior Ponderosa Pine — First Findings from Blacks Mountain Interdisciplinary Research.

A common, but largely untested, strategy for maintaining forest biodiversity is to enhance stand structural complexity. A silvicultural experiment was implemented from 1996 to 1998 at Blacks Mountain Experimental Forest, California, to test the efficacy of two levels of structural diversity (high versus low) and two levels of prescribed underburning (burn versus no burn) for maintaining or restoring biodiversity. Small mammals were trapped and tagged in experimental units for 2 noncontiguous weeks in fall 2003 and 2004. Total number of captures and number of captured individuals varied by year (P < 0.002). No treatment effects were detected for all species lumped together or for the three most frequent species analyzed separately ( Tamias amoenus J.A. Allen, 1890, Peromyscus maniculatus (Wagner, 1845), and Spermophilus lateralis (Say, 1823)), with the exception that T. amoenus was captured more often in burned units in 2004 (P = 0.004 for year × burn interaction). Mixed-effects regression models indicated that the number of captures and captured individuals of T. amoenus and P. maniculatus decreased with increasing residual basal area of overstory trees, but opposite results were obtained for S. lateralis. After accounting for residual stand density differences, T. amoenus was captured more frequently in units of low structural diversity and S. lateralis in units of high structural diversity.